The Scottish Government is to consult on whether older pupils should be allowed to opt themselves out of religious observance at school.
The Humanist Society of Scotland (HSS) is seeking a judicial review of current policy, which requires all children to have parental permission.
In England and Wales older pupils aged 16 to 18 are able to decide themselves whether to opt out of activities such as religious assemblies.
The HHS wants young people in Scotland to be given the same right, and accused Scottish ministers of acting unlawfully.
A United Nations committee has called for pupils to be given the independent right of withdrawal from any religious worship held in schools.
The HSS application for judicial review was approved, but now the Court of Session has granted a motion to halt the legal action for three months.
The motion was put forward by the Government with the consent of the HSS.
The Government intends to use the three-month period to consult with key groups on changes to religious observance in schools guidance.
A Government spokesman said: “We believe religious observance in schools should support the values of a diverse, outward-looking Scotland, which encourages young people to develop their own beliefs and values and understand and respect the beliefs and values of others.
“Listening to the views of young people themselves on all aspects of education is very important, as we have clearly recognised through our approach in the Children and Young People (Scotland) Act 2014 and the current Education Governance Review.
“We welcome the opportunity to work with key interests to discuss how we ensure this approach is fully reflected through religious observance guidance.”